The Vermont transportation secretary has started an investigation into the Vermont Rail Systems after a letter from Amtrak called the Rutland to Whitehall track owned by the company “the poorest performing line in the country.”

Secretary Brian Searles said he is concerned the issue could damage the state’s chances of getting a $74 million grant to upgrade its western rail corridor and extend passenger service from Rutland to Burlington.

The track used by Amtrak, for its Rutland-to-New York City “Ethan Allen Express” service was the site of a Jan. 29 derailment of a Vermont Rail freight train, which canceled the Ethan Allen for that day.

The main issue with the poor on-time performance of the Ethan Allen on Vermont Rail’s Clarendon and Pittsford (CLP) line, concerns “slow orders” issued by the rail company for safety reasons.

“Amtrak is concerned about the condition of the CLP,” Searles said. “It’s at less than 70 percent on-time, and it’s mainly because of the slow orders that go out when there are track issues.”

The state is getting ready for its third application for grant funds so it can work with Vermont Rail to improve services on the lines in western Vermont, starting with the Rutland-to-Burlington line. The next step would be to connect Rutland to Bennington by rail.

Vermont Rail President Dave Wulfson said the letter did not contain any new information, as far as his company was concerned.

“We have been working with Amtrak on an improvement plan. They are using a new formula to come up with information on delays, and that makes the railroads more accountable. We have been meeting with them on that.

“That’s all in the works. That letter was just meant to be informational,” he said. “There’s nothing new in any of that.”

The letter came from Stephen Gardner, the vice president of policy and development for Amtrak and said, Vermont Rail “remains unwilling to meet its ongoing obligations to adequately maintain the rail line.”

The letter documented issues going back to 2006 with “slow orders” on the line. It also attributes 91 percent of the Ethan Allen’s delays to those orders.

Wulfson pointed out that the section of track Vermont Rail owns on the Ethan Allen run is only 25 miles long,

“It’s probably the smallest chunk of track that they run over. Seven minutes a day is what the delay is coming to. We only have 25 miles of track, and there’s no chance to make up the time.”

Wulfson said Vermont Rail crews should start improvement work on the seven miles of track from Whitehall to the Vermont border in June. That work is coming from a $1.5 million grant from the New York Department of Transportation

The Ethan Allen service does not stop in Whitehall but rather travels directly through town. The closest stop is Castleton, Vt., and then it goes south to Fort Edwards, Saratoga Springs and Albany/Rensselaer before the rest of its scheduled five hour and 30 minute run to Penn Station.

The Amtrak train that stops in Whitehall is the Adirondack, which runs from Penn Station to Montreal but does not use the Vermont Rail tracks.

Until 1995, there was also an Amtrak train that ran from New York City to Montreal through Vermont.

The route was shortened after labor and other issues, Searles said. The Vermonter, which connects New York and Burlington, now ends in St. Albans instead of going across the border.